6SYN | pdb_00006syn

Crystal structure of Y. pestis penicillin-binding protein 3

• PDB DOI: https://doi.org/10.2210/pdb6SYN/pdb

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-09-30 Released: 2020-10-14 
• Deposition Author(s): Pankov, G., Hunter, W.N., Dawson, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 
  0.273 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

The structure of penicillin-binding protein 3 from Yersinia pestis

Pankov, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 58.15 kDa 
• Atom Count: 3,752 
• Modeled Residue Count: 471 
• Deposited Residue Count: 533 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan D,D-transpeptidase FtsI	A	533	Yersinia pestis	Mutation(s): 0  Gene Names: ftsI, YPO0549 EC: 3.4.16.4
UniProt
Find proteins for A0A3N4B5A3 (Yersinia pestis) Explore A0A3N4B5A3  Go to UniProtKB:  A0A3N4B5A3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CB9	D [auth A]	(2R,4S)-2-[(1R)-1-{[(2S)-2-carboxy-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid C17 H20 N2 O6 S YABPSSAFCROUQF-OWTLIXCDSA-N
ACT	B [auth A], C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free:  0.273 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.86	α = 90
b = 104.95	β = 90
c = 110.42	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-10-14 
Deposition Author(s): Pankov, G., Hunter, W.N., Dawson, A.

Revision History  

• Version 1.0: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary